RL2 - BACSU - GREMLIN Contacts

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RL2 - 50S ribosomal protein L2

UniProt:	P42919	Sequences: MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKRQYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGPEADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGEVRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	277 (273)
Sequences:	2461 (987)
Seq/√Len:	59.7

ECOLI - RL2
BACSU - RL2
HALSA - RL2
SULSO - RL2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_G	94_I	3.718	1.00
150_K	153_Q	3.514	1.00
79_A	95_N	3.164	1.00
72_D	189_R	3.051	1.00
26_T	80_T	3.019	1.00
164_V	172_V	2.934	1.00
53_H	219_T	2.927	1.00
172_V	186_S	2.880	1.00
143_N	152_G	2.831	1.00
139_T	192_I	2.759	1.00
223_S	240_P	2.651	1.00
141_V	164_V	2.636	1.00
155_V	162_A	2.600	1.00
141_V	174_V	2.568	1.00
58_H	213_W	2.548	1.00
216_I	219_T	2.546	1.00
144_I	162_A	2.539	1.00
94_I	116_I	2.370	1.00
133_I	187_A	2.355	1.00
174_V	184_I	2.349	1.00
108_K	198_E	2.310	1.00
37_L	60_R	2.200	1.00
105_L	152_G	2.174	1.00
70_D	102_R	2.108	1.00
110_I	116_I	2.105	1.00
129_A	189_R	2.093	1.00
88_S	200_H	2.093	1.00
71_K	98_D	2.081	1.00
253_P	257_F	2.080	1.00
262_K	266_S	2.050	1.00
44_N	50_T	2.042	1.00
173_L	181_V	2.041	1.00
243_R	247_M	2.036	1.00
241_I	255_L	2.003	1.00
194_Q	198_E	1.999	1.00
111_Q	114_T	1.969	1.00
71_K	100_E	1.906	1.00
54_Q	216_I	1.878	1.00
170_K	185_L	1.849	1.00
135_I	192_I	1.818	1.00
205_I	211_S	1.805	0.99
248_S	252_K	1.788	0.99
9_T	13_R	1.786	0.99
95_N	101_K	1.734	0.99
27_D	80_T	1.705	0.99
131_P	134_N	1.666	0.99
51_V	219_T	1.663	0.99
211_S	214_K	1.652	0.99
77_R	95_N	1.639	0.99
19_S	90_N	1.638	0.99
107_P	110_I	1.627	0.99
6_Y	18_T	1.624	0.99
19_S	203_I	1.600	0.99
144_I	174_V	1.598	0.99
154_L	184_I	1.575	0.99
35_A	64_V	1.575	0.99
78_V	110_I	1.573	0.99
40_K	54_Q	1.573	0.99
92_A	106_A	1.558	0.98
254_T	257_F	1.557	0.98
223_S	239_A	1.555	0.98
114_T	125_K	1.554	0.98
13_R	16_M	1.551	0.98
30_E	101_K	1.529	0.98
75_P	115_E	1.508	0.98
240_P	255_L	1.507	0.98
77_R	115_E	1.507	0.98
205_I	214_K	1.492	0.98
119_G	122_A	1.486	0.98
166_G	173_L	1.485	0.98
108_K	194_Q	1.482	0.98
167_K	186_S	1.458	0.98
223_S	241_I	1.443	0.98
90_N	196_G	1.443	0.98
73_G	119_G	1.437	0.97
78_V	94_I	1.435	0.97
232_H	247_M	1.432	0.97
122_A	130_L	1.428	0.97
261_K	267_D	1.428	0.97
72_D	118_S	1.424	0.97
146_L	184_I	1.419	0.97
79_A	101_K	1.418	0.97
89_A	195_V	1.394	0.97
241_I	245_S	1.385	0.97
173_L	183_M	1.377	0.97
34_L	61_Q	1.366	0.97
252_K	257_F	1.352	0.96
73_G	121_E	1.349	0.96
105_L	143_N	1.328	0.96
171_Y	185_L	1.310	0.96
2_A	20_D	1.306	0.95
133_I	186_S	1.304	0.95
145_E	151_G	1.299	0.95
24_I	27_D	1.281	0.95
148_P	185_L	1.262	0.95
72_D	119_G	1.257	0.94
65_I	91_I	1.250	0.94
75_P	97_A	1.247	0.94
130_L	135_I	1.232	0.94
154_L	176_L	1.223	0.94
21_F	90_N	1.206	0.93
10_S	13_R	1.201	0.93
140_V	161_S	1.199	0.93
54_Q	219_T	1.185	0.92
108_K	196_G	1.185	0.92
147_K	150_K	1.177	0.92
60_R	86_N	1.170	0.92
25_T	80_T	1.167	0.92
239_A	243_R	1.141	0.91
220_V	224_V	1.133	0.91
146_L	154_L	1.128	0.91
74_I	97_A	1.127	0.90
15_G	204_N	1.118	0.90
240_P	243_R	1.111	0.90
3_I	17_T	1.103	0.90
53_H	216_I	1.097	0.89
107_P	142_H	1.096	0.89
232_H	241_I	1.093	0.89
173_L	271_V	1.086	0.89
21_F	203_I	1.079	0.88
53_H	220_V	1.078	0.88
245_S	255_L	1.071	0.88
105_L	195_V	1.067	0.88
4_K	18_T	1.059	0.88
6_Y	16_M	1.056	0.87
226_N	229_D	1.045	0.87
41_G	54_Q	1.042	0.87
248_S	255_L	1.039	0.86
12_G	16_M	1.038	0.86
210_R	214_K	1.022	0.86
28_K	61_Q	1.021	0.86
232_H	240_P	1.013	0.85
121_E	130_L	1.006	0.85
211_S	216_I	1.002	0.84
52_R	225_M	0.997	0.84
223_S	245_S	0.991	0.84
77_R	97_A	0.990	0.84
129_A	191_S	0.989	0.84
71_K	96_Y	0.981	0.83
219_T	232_H	0.975	0.83
38_H	41_G	0.973	0.83
252_K	255_L	0.973	0.83
266_S	269_F	0.968	0.82
25_T	81_V	0.959	0.82
267_D	273_R	0.947	0.81
9_T	12_G	0.946	0.81
121_E	134_N	0.946	0.81
185_L	269_F	0.939	0.80
232_H	254_T	0.931	0.80
135_I	164_V	0.929	0.80
170_K	186_S	0.927	0.79
6_Y	10_S	0.927	0.79
262_K	267_D	0.922	0.79
228_N	241_I	0.918	0.79
92_A	110_I	0.913	0.78
199_Q	202_L	0.912	0.78
236_E	240_P	0.908	0.78
80_T	112_V	0.906	0.78
25_T	112_V	0.904	0.78
74_I	100_E	0.900	0.77
24_I	28_K	0.900	0.77
76_G	102_R	0.893	0.77
10_S	16_M	0.891	0.77
51_V	54_Q	0.886	0.76
36_P	61_Q	0.883	0.76
53_H	217_R	0.880	0.76
167_K	172_V	0.877	0.76
75_P	117_M	0.874	0.75
6_Y	13_R	0.873	0.75
80_T	92_A	0.873	0.75
261_K	264_N	0.870	0.75
135_I	190_A	0.861	0.74
120_P	130_L	0.849	0.73
171_Y	269_F	0.848	0.73
24_I	90_N	0.847	0.73
18_T	21_F	0.846	0.73
223_S	243_R	0.845	0.73
258_K	275_K	0.840	0.72
248_S	254_T	0.834	0.72
13_R	17_T	0.829	0.71
4_K	16_M	0.828	0.71
241_I	247_M	0.825	0.71
241_I	254_T	0.824	0.71
53_H	249_P	0.823	0.71
19_S	23_E	0.821	0.71
163_Q	175_R	0.817	0.70
120_P	134_N	0.815	0.70
44_N	48_K	0.808	0.69
144_I	155_V	0.806	0.69
118_S	189_R	0.804	0.69
245_S	254_T	0.798	0.68
119_G	130_L	0.796	0.68
73_G	117_M	0.796	0.68
33_L	93_L	0.795	0.68
104_I	142_H	0.794	0.68
6_Y	15_G	0.786	0.67
53_H	225_M	0.785	0.67
70_D	100_E	0.782	0.67
164_V	186_S	0.781	0.67
23_E	90_N	0.781	0.67
232_H	248_S	0.781	0.67
227_P	236_E	0.778	0.67
49_L	220_V	0.775	0.66
43_R	47_G	0.773	0.66
20_D	23_E	0.767	0.65
124_I	130_L	0.763	0.65
117_M	123_D	0.762	0.65
142_H	191_S	0.758	0.64
248_S	253_P	0.756	0.64
12_G	15_G	0.755	0.64
223_S	247_M	0.753	0.64
79_A	94_I	0.741	0.63
76_G	96_Y	0.740	0.63
88_S	106_A	0.738	0.62
228_N	255_L	0.737	0.62
155_V	160_T	0.736	0.62
81_V	91_I	0.735	0.62
256_G	259_T	0.735	0.62
225_M	229_D	0.735	0.62
110_I	142_H	0.732	0.62
205_I	210_R	0.732	0.62
62_Y	86_N	0.730	0.62
110_I	126_V	0.727	0.61
65_I	80_T	0.725	0.61
240_P	245_S	0.724	0.61
82_E	103_Y	0.722	0.61
228_N	245_S	0.722	0.61
71_K	102_R	0.721	0.61
155_V	174_V	0.720	0.61
57_G	60_R	0.719	0.60
104_I	107_P	0.719	0.60
3_I	49_L	0.719	0.60
18_T	203_I	0.716	0.60
142_H	195_V	0.715	0.60
239_A	247_M	0.714	0.60
21_F	58_H	0.714	0.60
132_L	174_V	0.713	0.60
37_L	62_Y	0.713	0.60
137_V	166_G	0.711	0.60
247_M	253_P	0.709	0.59
17_T	204_N	0.706	0.59
3_I	19_S	0.704	0.59
84_D	87_R	0.694	0.58
5_K	17_T	0.694	0.58
17_T	203_I	0.694	0.58
5_K	9_T	0.691	0.57
76_G	116_I	0.691	0.57
221_R	224_V	0.691	0.57
75_P	271_V	0.690	0.57
264_N	267_D	0.689	0.57
2_A	22_A	0.687	0.57
232_H	255_L	0.686	0.57
161_S	194_Q	0.685	0.57
69_R	142_H	0.681	0.56
4_K	13_R	0.678	0.56
227_P	247_M	0.675	0.56
49_L	53_H	0.674	0.55
123_D	201_E	0.669	0.55
222_G	232_H	0.667	0.55
240_P	248_S	0.666	0.55
141_V	144_I	0.666	0.55
51_V	220_V	0.663	0.54
94_I	196_G	0.662	0.54
99_G	151_G	0.661	0.54
258_K	273_R	0.657	0.54
44_N	47_G	0.656	0.53
97_A	115_E	0.656	0.53
16_M	196_G	0.655	0.53
9_T	16_M	0.654	0.53
237_G	240_P	0.652	0.53
223_S	255_L	0.651	0.53
81_V	92_A	0.650	0.53
7_K	125_K	0.649	0.53
120_P	133_I	0.645	0.52
263_K	266_S	0.645	0.52
54_Q	57_G	0.644	0.52
63_R	85_P	0.643	0.52
235_G	238_R	0.639	0.52
270_I	273_R	0.638	0.51
21_F	25_T	0.638	0.51
6_Y	17_T	0.636	0.51
8_P	14_R	0.633	0.51
36_P	60_R	0.631	0.51
5_K	12_G	0.631	0.51
73_G	120_P	0.630	0.51
94_I	102_R	0.629	0.50
137_V	167_K	0.625	0.50
94_I	110_I	0.624	0.50
109_G	179_G	0.624	0.50
69_R	104_I	0.620	0.49
118_S	129_A	0.619	0.49
164_V	167_K	0.618	0.49
50_T	148_P	0.617	0.49
55_G	60_R	0.616	0.49
131_P	187_A	0.615	0.49
53_H	250_W	0.613	0.49
77_R	113_G	0.609	0.48
40_K	51_V	0.608	0.48
119_G	189_R	0.605	0.48
123_D	189_R	0.605	0.48
261_K	268_K	0.604	0.48
263_K	269_F	0.604	0.48
141_V	162_A	0.603	0.48
213_W	216_I	0.602	0.47
155_V	177_N	0.601	0.47
49_L	219_T	0.601	0.47
24_I	81_V	0.600	0.47
45_N	50_T	0.600	0.47
10_S	14_R	0.600	0.47
69_R	129_A	0.599	0.47
39_K	54_Q	0.599	0.47
145_E	149_G	0.597	0.47
42_G	56_G	0.597	0.47
122_A	134_N	0.597	0.47
81_V	90_N	0.597	0.47
19_S	196_G	0.593	0.46
47_G	50_T	0.592	0.46
25_T	28_K	0.589	0.46
232_H	246_P	0.589	0.46
5_K	15_G	0.588	0.46
272_R	275_K	0.588	0.46
162_A	176_L	0.587	0.46
80_T	91_I	0.586	0.46
37_L	40_K	0.585	0.46
17_T	272_R	0.584	0.45
132_L	141_V	0.582	0.45
44_N	57_G	0.580	0.45
204_N	238_R	0.580	0.45
183_M	271_V	0.579	0.45
133_I	172_V	0.578	0.45
166_G	177_N	0.578	0.45
47_G	56_G	0.578	0.45
93_L	103_Y	0.577	0.45
137_V	258_K	0.574	0.44
224_V	247_M	0.574	0.44
120_P	131_P	0.572	0.44
80_T	101_K	0.571	0.44
24_I	80_T	0.571	0.44
71_K	74_I	0.571	0.44
4_K	31_K	0.571	0.44
21_F	24_I	0.569	0.44
80_T	196_G	0.569	0.44
152_G	191_S	0.568	0.44
19_S	24_I	0.567	0.44
74_I	261_K	0.567	0.44
29_P	34_L	0.567	0.44
247_M	254_T	0.567	0.44
27_D	112_V	0.563	0.43
10_S	22_A	0.563	0.43
88_S	196_G	0.560	0.43
108_K	202_L	0.553	0.42
74_I	117_M	0.553	0.42
175_R	258_K	0.550	0.42
172_V	184_I	0.546	0.41
82_E	85_P	0.546	0.41
219_T	250_W	0.545	0.41
54_Q	60_R	0.545	0.41
35_A	62_Y	0.544	0.41
173_L	186_S	0.543	0.41
42_G	45_N	0.543	0.41
115_E	214_K	0.541	0.41
19_S	27_D	0.540	0.41
59_K	157_S	0.538	0.40
13_R	18_T	0.537	0.40
16_M	204_N	0.535	0.40
264_N	269_F	0.534	0.40
115_E	268_K	0.533	0.40
161_S	198_E	0.530	0.40
155_V	161_S	0.529	0.39
81_V	101_K	0.528	0.39
11_N	165_L	0.527	0.39
52_R	248_S	0.527	0.39
93_L	101_K	0.526	0.39
166_G	169_G	0.526	0.39
25_T	177_N	0.524	0.39
112_V	165_L	0.522	0.39
144_I	184_I	0.521	0.39
58_H	214_K	0.521	0.39
11_N	15_G	0.519	0.38
32_S	80_T	0.518	0.38
69_R	118_S	0.518	0.38
124_I	192_I	0.517	0.38
174_V	181_V	0.515	0.38
6_Y	9_T	0.514	0.38
5_K	16_M	0.513	0.38
96_Y	99_G	0.513	0.38
147_K	153_Q	0.513	0.38
261_K	269_F	0.512	0.38
203_I	210_R	0.512	0.38
146_L	174_V	0.512	0.38
229_D	237_G	0.511	0.38
58_H	211_S	0.510	0.37
198_E	201_E	0.510	0.37
21_F	28_K	0.507	0.37
130_L	134_N	0.506	0.37
45_N	51_V	0.506	0.37
108_K	272_R	0.506	0.37
32_S	101_K	0.505	0.37
150_K	274_R	0.505	0.37
132_L	164_V	0.505	0.37
80_T	93_L	0.504	0.37
71_K	99_G	0.504	0.37
16_M	203_I	0.504	0.37
238_R	274_R	0.503	0.37
157_S	160_T	0.502	0.37
174_V	273_R	0.502	0.37
88_S	157_S	0.502	0.37
219_T	249_P	0.501	0.36
105_L	142_H	0.501	0.36
15_G	239_A	0.500	0.36

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3j3wC	1	1	100	0.008	Contact Map
4rb6D	1	0.9892	100	0.012	Contact Map
4tp9C	1	0.0072	100	0.025	Contact Map
1vw3B	1	0.9892	100	0.031	Contact Map
3bboE	1	0.9567	100	0.032	Contact Map
1vq8A	1	0.8231	100	0.239	Contact Map
3j21B	1	0.8303	100	0.242	Contact Map
3j7yD	1	0.7978	100	0.247	Contact Map
4ujqD	1	0.8484	100	0.252	Contact Map
1vx7D	1	0.8375	100	0.254	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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